Student Publications

Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S. "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol. 2006;188(23):8259-71. PubMed PMC DOI

Payne SH, Loomis WF. "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryot Cell. 2006;5(2):272-6. PubMed PMC DOI

Price ND, Thiele I, Palsson BØ. "Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of 'loop law' thermodynamic constraints." Biophys J. 2006;90(11):3919-28. PubMed PMC DOI

Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC Jr, Ribeiro AA, Murphy RC, Ulevitch RJ, Fearns C, Reichart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA. "Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4." J Lipid Res. 2006;47(5):1097-111. PubMed DOI

Reed JL, Famili I, Thiele I, Palsson BO. "Towards multidimensional genome annotation." Nat Rev Genet. 2006;7(2):130-41. PubMed DOI

Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. "Systems approach to refining genome annotation." Proc Natl Acad Sci U S A. 2006;103(46):17480-4. PubMed PMC DOI

Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." J Biol. 2006;5(4):11. PubMed PMC DOI

Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56. PubMed DOI

Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. "A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360. PubMed PMC DOI

Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72. PubMed DOI

Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL. "O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry." Mol Cell Proteomics. 2006;5(5):923-34. PubMed DOI

Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?." J Proteome Res. 2006;5(10):2554-66. PubMed PMC DOI

Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, Smith RD, Aebersold R. "UniPep--a database for human N-linked glycosites: a resource for biomarker discovery." Genome Biol. 2006;7(8):R73. PubMed PMC DOI

Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. "Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460. PubMed PMC DOI

Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. "Identifying repeat domains in large genomes." Genome Biol. 2006;7(1):R7. PubMed PMC DOI

Barken D, Wang CJ, Kearns J, Cheong R, Hoffmann A, Levchenko A. "Comment on 'Oscillations in NF-kappaB signaling control the dynamics of gene expression'." Science. 2005;308(5718):52; author reply 52. PubMed PMC DOI

Bashir A, Ye C, Price AL, Bafna V. "Orthologous repeats and mammalian phylogenetic inference." Genome Res. 2005;15(7):998-1006. PubMed PMC DOI

Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9. PubMed DOI

Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7. PubMed DOI

Devaraj NK, Miller GP, Ebina W, Kakaradov B, Collman JP, Kool ET, Chidsey CE. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J Am Chem Soc. 2005;127(24):8600-1. PubMed PMC DOI

Famili I, Mahadevan R, Palsson BO. "k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys J. 2005;88(3):1616-25. PubMed PMC DOI

Fong SS, Joyce AR, Palsson BØ. "Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states." Genome Res. 2005;15(10):1365-72. PubMed PMC DOI

Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat Chem Biol. 2005;1(4):191-2. PubMed DOI

Frank A, Tanner S, Bafna V, Pevzner P. "Peptide sequence tags for fast database search in mass-spectrometry." J Proteome Res. 2005;4(4):1287-95. PubMed DOI

Herrgård MJ, Palsson BØ. "Untangling the web of functional and physical interactions in yeast." J Biol. 2005;4(2):5. PubMed PMC DOI